Inhibiting APOBEC3 Activity with Single-Stranded DNA Containing 2


Nov 12, 2018 - APOBEC3 enzymes form part of the innate immune system by deaminating ... that range from active degradation (HIV-1 and related lentivir...
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Inhibiting APOBEC3 activity with single-stranded DNA containing 2'-deoxyzebularine analogs Maksim Vyacheslavovich Kvach, Fareeda M. Barzak, Stefan Harjes, Henry A. M. Schares, Geoffrey B. Jameson, Alex M. Ayoub, Ramkumar Moorthy, Hideki Aihara, Reuben S. Harris, Vyacheslav Filichev, Daniel A. Harki, and Elena Harjes Biochemistry, Just Accepted Manuscript • DOI: 10.1021/acs.biochem.8b00858 • Publication Date (Web): 12 Nov 2018 Downloaded from http://pubs.acs.org on November 13, 2018

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Biochemistry

For Table of Contents use only 239x137mm (96 x 96 DPI)

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Inhibiting APOBEC3 activity with single-stranded DNA containing 2'-deoxyzebularine analogs Maksim V. Kvach1#, Fareeda M. Barzak1#, Stefan Harjes1#, Henry A. M. Schares3#, Geoffrey B. Jameson1,2, Alex M. Ayoub3, Ramkumar Moorthy3, Hideki Aihara4, Reuben S. Harris4,5, Vyacheslav V. Filichev1,2*, Daniel A. Harki3*, Elena Harjes1,2* 1

Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, New

Zealand; 2 Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand; 3 Department of Medicinal Chemistry, 4 Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; 5 Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA. #

These authors contribute equally to this work.

*E-mail: [email protected], [email protected], [email protected]

Abstract APOBEC3 enzymes form part of the innate immune system by deaminating cytosine to uracil in single-stranded DNA (ssDNA) and thereby preventing the spread of pathogenic genetic information. However, APOBEC mutagenesis is also exploited by viruses and cancer cells to increase rates of evolution, escape adaptive immune responses, and resist drugs. This raises the possibility of APOBEC3 inhibition as a strategy to augment existing antiviral and anticancer therapies. Here we show that, upon incorporation into short single-stranded (ss)DNAs, the cytidine nucleoside analog 2'deoxy-zebularine (dZ) becomes capable of inhibiting the catalytic activity of selected APOBEC variants derived from APOBEC3A, APOBEC3B, and APOBEC3G supporting a mechanism in which ssDNA delivers dZ to the active site. Multiple experimental approaches, including isothermal titration calorimetry, fluorescence polarization, protein thermal shift, and NMR spectroscopy assays demonstrate nanomolar dissociation constants and low micromolar inhibition constants. These dZ containing ssDNAs constitute the first substrate-like APOBEC3 inhibitors and, together, comprise a platform for developing nucleic acid-based inhibitors with cellular activity.

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Biochemistry

Introduction Enzymes of the human APOBEC3 (A3A-H) family normally combat retroviruses and other pathogenic elements by deaminating 2'-deoxycytidine to 2'-deoxyuridine in single-stranded (ss)DNA (Figure 1A). The combination of this deamination-dependent mechanism and a deaminationindependent mechanism1, most likely dependent on nucleic acid binding, constitutes a potent block to parasite replication. Not surprisingly, viral pathogens have developed A3 counteraction strategies that range from active degradation (HIV-1 and related lentiviruses)1-4 to apparently passive avoidance (papilloma viruses and polyomaviruses)5, 6. Moreover, the fact that many immune-escape and drugresistance mutations occur within A3-preferred di- and tri-nucleotide motifs7-10 strongly suggest that viruses have evolved mechanisms to both regulate and benefit from A3 mutagenesis. A3 enzymes have intrinsic preferences for deaminating cytosine bases preceded by thymine (5'-TC, A3A-D, A3F, and A3H) or by another cytosine (5'-CC, A3G)10-14. The genomes of many different tumor types, including bladder, breast, cervix, head/neck, and lung, often have large fractions of mutations in 5'-TC motifs15-17. These 5'-TC-to-TT and 5'-TC-to-TG mutations are typically followed on the 3'-side by bases other than cytosine, that is adenine, guanine, or thymine, thereby constituting an APOBEC mutation signature. A range of genetic, biochemical, and structural studies have combined to implicate A3B as the primary source of these mutations, and A3A and A3H as potential secondary sources (depending on patient genotype and tumor type). APOBEC mutagenesis has been shown to contribute to both clonal and subclonal mutational events17, 18 and its frequency often increases from primary to metastatic disease16. A3B expression levels and APOBEC signature mutations also correlate with poor clinical outcomes including disease recurrence, metastasis, and drug resistance15, 19, 20. These observations support a model in which APOBEC mutagenesis promotes tumor evolution and strongly influences disease trajectories. Therefore, chemical modulators of APOBEC activity may yield useful chemical probes for mechanistic studies, and possibly, therapeutic compounds to harness APOBEC mutagenesis21. The mechanism of cytosine deamination for APOBECs is thought to be similar to that for cytidine deaminase (CDA), an enzyme that processes individual nucleosides22. The cytidine analogs zebularine (Z, Figure 1B), 2'-deoxyzebularine (dZ), and tetrahydrouridine (THU) are known transition-state analogs (TSA) of cytidine deaminase (CDA)23-25. These competitive inhibitors bind tightly to the active site of CDA, as indicated by crystal structures23-28. Here we show that these TSAs as free nucleosides do not alter activity of A3 enzymes (Figure S1), but micromolar-potent A3 inhibitors are obtained upon introduction of dZ in place of the target 2'-deoxycytidine in DNA substrates (dZssDNA). These findings open new avenues for further investigations of interactions between active

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Biochemistry

A3 enzymes and ssDNA and, importantly, for the rational design of competitive A3 inhibitors for use with living cells. O

NH2

C

U

APOBEC3A-H

NH

N

O

O

B)

DN

NH3

H 2O

ss

DN

A

N

N

A

A)

ss

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

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N HO

N

N O

O

HO

OH OH

N O OH

Zebularine (Z)

O

dZ

OH N

NH HO

N O

O

HO

OH OH

N

O

O OH

dZMe

THU

Figure 1: A) Deamination of dC in ssDNA by A3 enzymes; B) TSAs used in this work: Zebularine, its 2'-deoxy analog (dZ) and 5-methyl-2'-deoxyzebularine (dZMe), tetrahydrouridine (THU). Materials and methods Detailed methods are provided in supplementary information. Synthesis of 2'-deoxyzebularine (dZ), its phosphoramidite and oligonucleotides containing dZ and dZMe. Synthetic procedures are provided in Supplementary Information. Protein expression and purification Human APOBEC3A (1-199, Uniprot code P31941) was cloned as the inactive E72A mutant with a His6 C-terminal fusion tag into an expression vector (pETite, Lucigen), expressed in Escherichia coli BL21 DE3 cells (Hi-Control, Lucigen) and purified as described29.

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Biochemistry

A3B C-terminal domain (residues 187 to 378) was cloned into pET24a vector (Novagen) to produce A3Bc proteins with a non-cleavable C-terminal His6-tag (LEHHHHHH) were derived from previously described study30. Several derivative constructs previously reported31 were used in this study, A3BCTD QM-∆L3, A3BCTD -QM-∆L3-E255A were expressed in E. coli strain BL21(DE3) (Lucigen), and A3BCTD -QM-∆L3-AL1swap expressed in the E. coli strain C41(DE3)pLysS (Lucigen). E. coli culture was grown at 37 °C in LB medium, once mid-log growth phase was established the culture supplemented with 100 µM zinc chloride, before inducing protein expression by the addition of isopropyl β-D-1-thiogalactopyranoside (IPTG) at a final concentration of 0.5 µM and incubating overnight at 18 °C. A3BCTD -DM was expressed and purified as reported in the recent paper31. A3GCTD (191-384, wt) was purified as described32. The glutathione S-transferase (GST)-fused A3GCTD was expressed in Escherichia coli BL21(DE3) cells overnight at 17°C. After harvesting, the cells were resuspended in 50 mM sodium phosphate buffer (pH 7.4) and lysed by sonication. After ultracentrifugation at 25,000 g for 10 min, the supernatant was added to glutathione (GSH)-Sepharose, which was subsequently washed. For kinetic analysis, the GST fusion protein was eluted from the Sepharose matrix with 100 mM GSH in phosphate buffer. By using filtration at 4,000 g, the buffer was changed to a solution containing 75 mM sodium phosphate and 75 mM citrate, at pH 5.5. Fluorescence polarization assay Fluorescence polarization assays were performed with recombinant (purified from E. coli strain BL21[DE3]), A3A (amino acids 1-195, expressed using the pGEX vector as a GST-fusion)30 with the catalytic glutamic acid mutated to alanine (E72A) to render the enzyme unable to deaminate substrate. The assay buffer consisted of 2-(N-morpholino)ethanesulfonic acid (MES; 50 mM, aq.), NaCl (100 mM, aq.), tris(2-carboxyethyl)phosphine (TCEP; 2 mM, aq.), and 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS; 4 mM, aq.) at pH 6.0. 15 µM stock solutions of fluorescent tracer 5'-(6-FAM)TTTTCAT (Integrated DNA Technologies; MW = 2,598.3 g/mol) in molecular biology grade water were diluted to 15 nM in assay buffer. All FP experiments were performed with a 10 µL assay volume in black round bottom low-volume 384-well plates (Corning 4514). A direct binding experiment (Chart S3) was first performed to determine the Kd of 5'-(6FAM)TTTTCAT-3' to A3A-E72A by serially diluting the protein (1:1, 10 µM starting concentration) and incubating with constant concentration (15 nM) of fluorescent tracer. Plates were incubated at room temperature for 30 minutes, gently shaken for 1 minute, and then analyzed for fluorescence polarization on a BioTek Synergy 2 instrument (using standard instrument settings) with an excitation wavelength of 485 (20) nm, an emission wavelength of 528 (20) nm, and the top optics position at 510 nm. The resulting anisotropy values were fit using the one-site binding (hyperbola) function in GraphPad Prism 7.0 to obtain the Kd of the fluorescent tracer. The directly measured Kd was 18.2 ± 1.0 nM (Chart S3). This value was used for all further calculations. Competition binding experiments were then performed 4 ACS Paragon Plus Environment

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with the pre-bound fluorescent tracer and various test ligands to quantify their binding affinities, as described in Supporting Information. Isothermal titration calorimetry Desalted unmodified DNA oligonucleotides were purchased (Integrated DNA Technologies) at 1 or 5 µmol synthesis scale and dissolved in one of the buffers described below to give 10 mM solutions. ITC experiments were conducted at 25 °C using a Micro-Cal ITC200 (now Malvern Instruments) isothermal titration calorimeter. A3A-E72A (130 µM in high salt or medium salt buffer) or A3BCTD -QM-∆L3AL1swap (100 µM, activity assay buffer) was titrated in corresponding buffer. DNA oligonucleotides at 1.6 mM (for A3A-E72A) or 300 µM (for A3BCTD -QM-∆L3-AL1swap) concentration were added in 18 steps at 2.0 µL each (plus a first addition with reduced volume of 0.4 µL to prevent dilution of the DNA in the syringe due to the long wait before the start of the experiment). Oligos and the enzymes were dialyzed against the appropriate buffer. Buffers used are given below: For A3A-E72A: High salt buffer consists of 25 mM sodium phosphate, 500 mM NaCl, 300 mM choline acetate, 5 mM β-mercaptoethanol and 0.2 mM Na2-EDTA, pH 6.0 or medium salt buffer consists of 50 mM MES, 100 mM NaCl, 2.0 mM tris(2-carboxyethyl)phosphine, pH 6.0. For A3BCTD -QM-∆L3-AL1swap: Activity assay buffer consists of 50 mM citrate-phosphate buffer, 200 mM NaCl, 2 mM β-mercaptoethanol, pH 5.5. Thermal Shift Assay A fluorescence-based thermal shift assay was used to assess binding capability of ssDNA oligonucleotides to A3BCTD proteins, through examination of changes in the proteins thermal stability. Binding assays were conducted using inactive A3BCTD protein constructs, A3BCTD-QM-ΔL3 and A3BCTD-QM-ΔL3 (E255A), where dC substrate is not converted to dU, and to determine if differences in binding affinity occur due to a single amino acid change (E255A) in the protein. Purified A3BCTD protein was appropriately diluted in buffer (50 mM citrate-phosphate pH 5.5, 200 mM NaCl, 2 mM βmercaptoethanol, pH 5.5, 200 µM 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS)). Assay experiments were setup in a total volume of 25 µl containing; 20 µM A3BCTD protein, 100 µM ssDNA oligonucleotide, mixed with SYPRO® orange dye (BioRad) at a final concentration of 10X. Assays were dispensed into wells of a white Low-Profile 96-Well plate (Roche) then sealed with optical seal, shaken, and centrifuged. Thermal scanning (20 to 95°C at 0.6°C/min) was performed using a real-time PCR setup on a LightCycler 480 instrument II (Roche) with fluorescence emission spectra recorded with combinations of excitation and emission filters (483–610 and 483–568 nm, respectively). Evaluation of nucleosides by fluorescence-based deamination assay using hA3A and hA3BCTD expressed in HEK293T cells

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Biochemistry

A3-deaminase activity assays were performed according to Li and colleagues33 with the following modifications. Stock solutions of nucleosides in molecular biology grade water were serially diluted in protein dilution buffer (10 µL). Recombinant (purified from HEK293T cells) full length A3A-mycHis33 (10 ng) or C-terminal domain (amino acids 195-382) A3BCTD-mycHis34,

35

(25 ng) proteins were

delivered to each well in protein dilution buffer (10 µL). The deamination dual-fluorophoric substrate oligo 5'-(6-FAM)-AAA-TAT-CCC-AAA-GAG-AGA-(TAMRA) (2 pmol) and UDG (25 units) were delivered in TE buffer (10 µL). Cleavage of oligonucleotides containing an abasic site using NaOH (4 M, 3 µL) occurred after 30 min reaction incubation at 37 °C. Plates were read using BioTek Synergy H1 plate reader with an excitation wavelength at 490 nm and emission at 520 nm. Each experiment was performed in biological duplicate with three technical replicates per condition. Resulting total fluorescence values were reported together with the no-protein low control and protein only high control (no inhibitors). Unspecific inhibitor MN-1 was used as a positive control. (Figure S1)33. Evaluation of inhibitors in NMR-based assay The Supplementary information provides details of experiments and how inhibition constants were calculated. Results Methodology of this investigation First, we confirmed that pyrimidine-based TSA nucleosides (Fig. 1B) do not inhibit A3 enzymes (Figure S1). Since ssDNA is the preferred substrate of A3 proteins, we then decided to evaluate the inhibitory effect of chemically modified ssDNAs in which the target 2'-deoxycytidine in the recognition sequence32, 36 is substituted with TSAs. We focused on 2'-deoxyzebularine (dZ), as it is a known, stable, moderately potent TSA inhibitor of CDA with an apparent Ki of 2.9 µM37 and its incorporation into DNA by automated synthesis is feasible38. The quantity of modified oligos needed for the planned experiments warranted development of a new synthesis procedure for dZ. Then, we investigated binding affinity and inhibitory activity of selected modified oligos. Binding data was determined using a combination of fluorescence polarization (FP), isothermal calorimetry (ITC) and thermal shift assays. We confirmed that 9-10 nucleotides is a good compromise between length of the oligo and binding affinity, and concluded that binding of TSA-containing oligos must be investigated with catalytically active proteins. Finally, our activity data show clearly the inhibition of selected A3-variants by dZcontaining oligos. The list of proteins used can be found in Figure S3 in the Supporting Information, and the sequences of oligos in Tables 1 and 2. One should note that the preferred A3G substrate motif is CCCA (underlined C preferentially deaminated), whereas A3A and A3B prefer the TCA motif, but

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can also readily deaminate CCCA motif. The rationale for the design of each oligo can be found in Table S3 in the Supporting Information. A3 activity is unaffected by free nucleoside transition-state analogs Human A3A and the catalytic C-terminal domain of A3B (A3BCTD were purified from human 293T cells (hA3A, hA3BCTD) 33 and tested using a fluorescence-based activity assay33 (for details see Methods and Supplementary Information) for inhibition by nucleosides THU, Z, and dZ. The non-specific small molecule inhibitor MN-133 almost completely abolished activity of enzymes used in the assay (hA3A, hA3BCTD and UDG). In contrast, THU, Z, and dZ did not affect the deamination of ssDNA by these enzymes, even at the high concentration of 2 mM (Figure S1). These results are consistent with earlier observations of no or very weak binding of A3 proteins to individual nucleotides and barely detectable deamination of 2'-deoxycytidine39, 40 Synthesis of dZ-containing ssDNA We developed a new straightforward procedure to prepare dZ phosphoramidite for incorporation into ssDNA based on the classical silyl modification of the Hilbert-Johnson reaction (Scheme 1 and Supplementary information). This synthesis, which is Lewis acid-free and requires no workup, leads straightforwardly to the product 3a, which was purified by flash chromatography. We obtained a much higher ratio and yield of the desired β anomer (β:α = 88:12) than the previously published procedure38, 41

. dZ was further used in the synthesis of modified 2'-oligodeoxynucleotides (Oligos) as described in

SI. Commercially available phosphoramidite of 5-methyl-2'-deoxyzebularine was used in the synthesis of dZMe-containing oligos.

O TolO

Cl

TolO 1: Tol = 4-MeC6H4CO

N

+ N 2

i

OTMS

O RO

N

RO ii

N

iii

O DmtO

O

3a: R = Tol 3b: R = H

RO iv

N

N O

4a: R = H 4b: R = P(OCH2CH2CN)NiPr2

Scheme 1: Reagents and conditions: i, CHCl3, distill., 10 min, 54%, α/β=12:88 (3a); ii, 28% aq. ammonia, MeOH, 48 h, (3b); iii, 4,4'-dimethoxytritylchloride, pyridine, 0°C→r.t., overnight, 54% (4a); iv, N,N-diisopropylamino-2-cyanoethoxychlorophosphine, Et3N, CH2Cl2, 30 min, 88% (4b).

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Biochemistry

Binding of modified and unmodified ssDNAs to A3 proteins We tested how the introduction of dZ and its 5-methyl derivative dZMe affected the affinity of ssDNA to the A3 enzymes, in particular to A3A and the catalytically competent A3BCTD and selected mutants, to probe the generality of zebularine analogs as inhibitors of A3 proteins. Given that different A3 proteins13, 36 have varying preferences for nucleobases surrounding the target cytosine, the sequences surrounding the zebularine moiety were chosen in order to match preferred ssDNA recognition motif. To study A3-ssDNA binding, we used the inactive A3A-E72A mutant, where the active-site glutamic acid is replaced by alanine, to avoid complications of deamination reactions occurring when the ligand contained cytosine. The E72A mutation does not change the geometry of the active side, as water was observed in the crystal structure instead of the glutamate side chain42. As A3A is a highly active enzyme with the highest affinity to DNA among human A3 catalytically active domains29, 36, it is best suited for binding assays. Two methods widely applied for binding characterization were used: fluorescence polarization (FP) and isothermal titration calorimetry (ITC), which yield, respectively, the indirectly determined dissociation constant KdFP (sometimes referred as Ki; see SI) 43-45 and the directly measured dissociation constant KdITC. FP measurements were carried out in competitive mode, where unlabelled ssDNA competed with the fluorescently labelled ssDNA for the protein (Figure S2; see SI). This results in dissociation constants KdFP (Table 1) that should be directly comparable with KdITC, on the assumption that the binding of the unlabelled and fluorescently labelled ssDNA to the protein are identical. As a positive control, KdFP for the non-labelled ssDNA (Oligo-10) was 34 ± 2 nM compared to the directly measured value of 19 ± 2 nM for titration of the fluorescently tagged Oligo-10. The differences between the two values are likely attributable to the experimental conditions (competitive displacement with a non-labeled Oligo versus direct binding with a fluorescently-labeled Oligo, respectively). Weaker binding of ssDNA containing dU (Oligo-11, KdFP =1800 ± 300 nM), as a negative control, compared to dC accords with published data29,46, 47 and highlights the binding specificity. The dZ-modified DNA had lower affinity to A3AE72A than the dC-containing substrate (Oligo-15, KdFP = 290 ± 20 nM, vs Oligo-10, KdFP= 34 ± 2 nM, Table 1 and vide subra). The affinity of the dZ-modified DNA was still substantially higher than that of the dU-containing ssDNA that mimics the product of deamination (Oligo-15 vs Oligo-11, Table 1). The comparison between Oligos-10, 12, 13 and 14 shows some increase of binding from seven to ten nucleotides length and no further increase of binding up to 13 nucleotides (Oligo-13).

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Table 1: Oligo concentration when the fluorescence anisotropy decreased to the half maximum level (IC50) and indirectly measured dissociation constants (KdFP) of ssDNA from A3A-E72A obtained in fluorescence polarisation (FP) experiments in a medium salt buffer. # c

Oligo-3* Oligo-4* Oligo-5* Oligo-10* Oligo-11 Oligo-12 Oligo-13 Oligo-14 Oligo-15

a

b c

FP

DNA sequence, 5'-3'

IC50 , µM

Kd , µM

ATTCCCAATT

0.0550± 0.0011

0.007 ± 0.001

TTCCC CCCAA TTTTCAT

5.6 ± 0.8 1.8 ± 0.10 0.2800 ± 0.0016

0.68 ± 0.11 0.22 ± 0.02 0.034 ± 0.002

15.0 ± 1.9

1.8 ± 0.3

0.0960 ± 0.0012 0.120 ± 0.004 0.1400 ± 0.0022 2.40 ± 0.10

0.012 ± 0.001 0.015 ± 0.001 0.017 ± 0.001 0.29 ± 0.02

b

TTTTdUAT TTTTCATTTT AAAAATTCAAAGA TTCAAAAA TTTTdZAT

FP

Values shown are mean ± SEM (standard error of mean). IC50 values were converted to Kd values using the Kenakin equation (see SI) with appropriate error propagation. dU is 2'-deoxyuridine. Asterisk refers to oligos evaluated in both ITC and FP experiments.

ITC experiments29 (Table 2) were initially performed in a high salt buffer (800 mM ionic strength), which was necessary for sample stability over the multi-day, multi-dimensional NMR measurements29. For Oligo-1 (20-mer, A8T2CA9) and the much shorter Oligo-2 (9-mer, AT3CAT3) with a different sequence, very similar dissociation constants (KdITC) of 24 ± 7 µM and 25 ± 1 µM were obtained (Table 2), the former value being the same as reported29. Given the very marked differences to the FP dissociation constants, further studies proceeded in buffer with lower salt concentration (medium buffer, 150 mM ionic strength), comparable to that for FP measurements. The new KdITC values obtained for Oligo-1 and Oligo-2 were more than 100 times lower than values measured in the high-salt buffer (Table 2). Moreover, differences in binding were now evident, such that the 20-mer bound nearly twice as strongly as the 9-mer (KdITC = 0.11 ± 0.05 µM vs 0.20 ± 0.04 µM, respectively). Further shortening of the DNA sequence to 5 nucleotides resulted in decreased affinity to the protein (Oligo-4, -5 and -6 compared to Oligo-3 in Table 2), showing that binding affinity increases with the oligo length and confirming that a length of ~9-10 nucleotides is a good compromise between the length of oligo and binding affinity. This length is used here and previously in NMR activity assays32, 48.

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Biochemistry

Table 2. Dissociation constants (KdITC) of ssDNA from A3 enzymes obtained by isothermal calorimetry (ITC) in different buffersa. #

DNA sequence, 5'-3'

Oligo-1

AAAAAAAATTCAAAAAAAAA

Oligo-2

ATTTCATTT

Oligo-3* Oligo-4* Oligo-5* Oligo-6 Oligo-7 Oligo-8

b,c

Oligo-9 Oligo-10* Oligo-16 a

ATTCCCAATT TTCCC CCCAA TTCAT ATTCCdZAATT Me

ATTCCdZ AATT ATTTdZATTT TTTTCAT 5'-(6-FAM)TTT TCAT

Buffer

Enzyme

Kd

high salt med. salt high salt med. salt med. salt

A3A-E72A A3A-E72A A3A-E72A A3A-E72A A3A-E72A

24 ± 7 0.11 ± 0.05 25.3 ± 0.9 0.20 ± 0.04 0.24 ± 0.10

med. salt med. salt med. salt med. salt med. salt

A3A-E72A A3A-E72A A3A-E72A A3A-E72A A3A-E72A

5.0 ± 0.4 3.1 ± 0.4 0.48 ± 0.10 0.97 ± 0.15 1.7 ± 0.3

activity assay

A3Bc-QMΔL3AL1swap A3A-E72A A3A-E72A

5.5 ± 0.6

med. salt med. salt

ITC

, µM

0.27±0.04 0.41±0.04

High salt buffer: 25 mM sodium phosphate, 500 mM NaCl, 300 mM choline acetate, 5 mM β-

mercaptoethanol and 0.2 mM Na2-EDTA, pH 6.0; Medium salt buffer: 50 mM MES, 100 mM NaCl, 2.0 mM tris(2-carboxyethyl)phosphine, pH 6.0. Activity assay buffer: 50 mM citrate-phosphate buffer, 200 mM NaCl, 2 mM β-mercaptoethanol, pH 5.5. Mean ± SD are shown. Uncertainties (SD) of KdITC were calculated using standard error-propagation methods from partial derivatives. b

Asterisk refers to oligos evaluated in both ITC and FP experiments.

c

A3A prefers to deaminate the third C in the CCC motif 36.

In general, KdFP values were somewhat lower than KdITC values (Table 1, Table 2), which is likely attributable to differences in experimental conditions: competition binding studies for KdFP versus direct binding experiments for KdITC. Additionally, the different concentrations of assay components used may contribute to different oligomeric states of the protein, thereby affecting the measured binding affinities. The oligomeric state of A3A-E72A under these conditions warrants further investigations. Nonetheless, consistent trends were observed between these two biophysical methods. Shortening of the oligo resulted in reduced binding to A3A-E72A in both methods (Oligos-4 and -5 vs Oligo-3, Table 1 and Table 2) consistent with the published data47. In parallel with FP results and despite different oligo sequences used, introduction of dZ into the ssDNA sequence (Oligo-7, KdITC = 10 ACS Paragon Plus Environment

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0.97 ± 0.15 µM) resulted in weaker binding, relative to the corresponding cytidine-containing ssDNA (Oligo-3, KdITC = 0.24 ± 0.10 µM), specifically, 8.5- and 4-fold increases in KdFP and KdITC, respectively, were observed (Table 2). The addition of a 5-methyl substituent to dZ (dZMe), Oligo-8, had negligible effect on binding relative to unmethylated Oligo-7 (Table 2). This impaired binding of transition-state analogs, dZ- or dZMe-ssDNA, to the E72A mutant, compared to substrate, is consistent with Glu72 being a critical residue in the formation of the transition state for active A3 enzymes. To test the importance of the catalytic glutamate (Glu72 in A3A), we evaluated binding of ssDNAs to two protein constructs of the catalytically active C-terminal domain of mutant A3B, A3BCTD-QM-ΔL3 (quadruple mutant with loop3 removed, Figure S3) and its catalytically inactive derivative A3BCTDQM-ΔL3-E255A30. For this experiment, we cannot use active A3A, the most potent A3 deaminase,36 as it will fully deaminate substrate during the experiment. The A3BCTD-QM-ΔL3 enzyme has the essential glutamic acid in the active site, but due to the removal of loop 3 is only very weakly active in vitro31: low conversion of the substrate to the product was detected by 1H-NMR spectroscopy only after incubation overnight (Figure S4). The TSA interaction with the active site is not likely to be affected by the deletion of loop 3 in these proteins, as the loss of deaminase activity and associated binding affinity is due to effects outside of the active site. Deaminase activity can be restored by swapping loop 1 of A3BCTD-QM-ΔL3 with loop 1 of A3A, yielding the active A3BCTD-QM-ΔL3 AL1swap enzyme31. On the other hand, in the A3BCTD-QM-ΔL3-E255A mutant the active-site glutamic acid (equivalent to Glu72 in A3A) is replaced with alanine. Therefore, these proteins provide a unique pair to evaluate the importance of the catalytic glutamate for binding of dZ-containing oligos. No binding of ssDNA to A3BCTD-QM-ΔL3 was seen by ITC under our standard conditions (50 mM citrate-phosphate buffer, 200 mM NaCl, 2 mM β-mercaptoethanol, pH 5.5), consistent with this mutant’s very low deaminase activity. Moreover, for a weak binding event such as this to be studied by ITC, the required concentration of the protein would be in the high µM range, which is prohibitive because A3 proteins tend to precipitate from solution at this concentration49. Consequently, we decided to use our previously published thermal shift assay29, where high ligand concentrations are used to enhance complex formation (Figure 2)50. Protein unfolding as temperature increases is reported by increased fluorescence of the non-polar dye SYPRO Orange, which binds to hydrophobic patches exposed on thermal denaturation. Usually, higher thermal stability is associated with the strong binding of the ligand, in our case ssDNA, to the protein. We observed that binding of oligos to inactive A3BCTD-QM-ΔL3-E255A is significantly lower than to weakly active A3BCTD-QM-ΔL3, which retains the catalytic glutamic acid. Moreover, for A3BCTD-QM-ΔL3, the ΔTm value for the dZcontaining Oligo-9 is 0.72 ( ±0.10) °C higher than that for the substrate containing dC (Figure 2, see 95% confidence interval), which is the expected result for an ssDNA that bears a TSA instead of dC. 11 ACS Paragon Plus Environment

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For the binding of inactivated A3BCTD-QM-ΔL3-E255A to different DNA oligos, the binding of dZ oligo cannot be distinguished from binding of the substrate, illustrating the importance of the activesite glutamate for binding of transition-state analogs.

Figure 2: Results of thermal shift assay for A3BCTD-QM-ΔL3 (green) and A3BCTD-QM-ΔL3-E255A (blue) in the presence of the product of deamination (5'-ATTTdUATTT), substrate (5'-dATTTCATTT) and dZ-containing Oligo-9 (dATTTdZATTT). Concentration of proteins was 20 µM, concentration of oligos was 100 µM in the buffer: 50 mM citrate-phosphate pH 5.5, 200 mM NaCl, 2 mM βmercaptoethanol, pH 5.5, 200 µM 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS). Confidence intervals (95%) are shown as error bars.

Altogether, these results demonstrate that the choice of buffer, especially the ionic strength, affects strongly, by several orders of magnitude, the affinity of ssDNA to the A3 proteins. Moreover, binding of inactive protein to ssDNA-containing TSA is not a reliable predictor of inhibitory potential of these oligonucleotides. Therefore, we decided to use our previously described NMR-based activity assay32 to assess directly the inhibition of substrate deamination in fully active A3 enzymes by ssDNA containing TSAs.

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2'-Deoxyzebularine incorporated into ssDNA is a µM inhibitor of A3 enzymes The Michaelis-Menten constants for the enzymes and their mutants used in this study (described in SI), along with their ssDNA substrates, are summarised in Table 3. The behaviour of the A3BCTD -QM∆L3-AL1swap30 (see description of the enzyme in Figure S3 in the Supporting Information), which has loop 1 of A3A transplanted into A3BCTD, was intermediate between previously reported activities for A3A40 and A3GCTD32, consistent with the previously reported data36. However, the kcat of A3BCTD-DM (DM: double mutant, see Supporting information, Figure S3) was anomalously low (0.008 ±0.001 s-1 compared to 0.10 ± 0.04 s-1 for A3GCTD32, Table 3). Residual enzyme activity in the presence of dZssDNA inhibitors was monitored directly by our NMR method32, 48. Table 3: Michaelis-Menten constants for selected A3 enzymes and mutants measured by the NMR assay.32, 40

Protein

Substrate

kcat , s

a

Oligo-3

A3A A3BCTD -QM-∆L3AL1swap c A3BCTD-DM c

Oligo-2

A3GCTD b

a

A3BCTD-QM-∆L3

c

Oligo-2 Oligo-2

-1

-1

Km , µM

kcat/Km , s µM

0.10 ± 0.04

570 ± 90

0.00018

1.2 ± 0.1

66 ± 7

0.018

0.28 ± 0.04

200 ± 30

0.0014

0.008 ± 0.001 320 ± 60 Barely active

-1

0.000025

See reference32 See also reference40 c See SI b

Only the use of dZ instead of dC in the preferred A3GCTD substrate (Oligo-7 versus Oligo-9, Figure 3A and B) conferred significant inhibition of A3GCTD deaminase activity. dZMe-ssDNA (Oligo-8) had a marginal effect on the conversion of the preferred A3GCTD substrate (AT2C3A2T2, Oligo-3) (Figure 3A). These data are consistent with 5-Me-cytidine being a much poorer substrate than cytidine for A3 proteins, with the exception of A3H51-53. Therefore, for further investigations we focused on evaluation of dZ-containing oligos. For both A3BCTD-QM-∆L3-AL1swap and A3BCTD-DM (Figure 3SI), using preferred substrate 5'-AT3CAT3 (Oligo-2), significant inhibition was observed with dZssDNA (Oligo-9, Figure 3C and -D). The linear dependence of inverse deamination speed on inhibitor concentration was analyzed as described in the Supplementary Information, on the assumption of competitive inhibition, yielding micromolar inhibition constants Ki (Figure 3B-D). In particular, for A3BCTD-QM-∆L3-AL1swap, the Ki and KdITC for Oligo-9, are very similar, respectively 7.5 ± 1.7 and 5.5 ± 0.6 µM (Figure 3C and Table 2). No binding of Oligo-7 (or any other oligo) to A3GCTD (or catalytic mutant) was seen by ITC (75 mM sodium phosphate and 75 mM citrate, pH 5.5) 13 ACS Paragon Plus Environment

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due to low DNA binding affinity to A3GCTD (Km(Oligo-3) ≈ 600 µM, Ki(Oligo-7) ≈ 50 µM) and low protein solubility.

Figure 3: Inhibition of A3 proteins by modified oligos in the NMR deaminase assay. A) Effects of dZ and dZMe-containing ssDNAs on deamination of Oligo-3 (dAT2C3A2T2, 500 µM) by A3GCTD (850 µM) at 298 K. Speed of deamination in the absence of inhibitor (No inhibitor) and in the presence of 100 µM ssDNA inhibitors (dZ-containing Oligo-7 and Oligo-9 as well as dZMe-containing Oligo-8) is shown. B) Inhibition of A3GCTD catalyzed deamination of Oligo-3 by dZ-containing Oligo-7. C) Inhibition of A3BCTD-QM-∆L3-AL1swap catalyzed deamination of Oligo-2 by dZ-containing Oligo-9. D) Inhibition of A3BCTD-DM catalysed deamination of Oligo-2 by dZ-containing Oligo-9. The bold C is the target 2'-deoxycytidine deaminated by the enzyme. In all cases, DNA substrate and inhibitor have the same sequence except that the cytidine of the substrate has been changed to dZ. To confirm the competitive nature of inhibition, substrate concentration was varied while keeping the inhibitor (Oligo-9) and enzyme (A3BCTD -QM-∆L3-AL1swap) concentrations constant. In the doublereciprocal plot shown in Figure 4, the lines from the least-squares fits to the data in the absence and in the presence of inhibitor cross the y-axis at essentially the same point (1/vmax = 71 ± 12 s µM-1 and 1/vmax = 83 ± 32 s µM-1, respectively). This result validates our initial prediction that dZ-ssDNAs are competitive inhibitors of A3 enzymes. 14 ACS Paragon Plus Environment

Biochemistry

1200 1000

1/V, s/µM

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

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800 600 400 200

-0.005

0

0

0.005

0.01

0.015

0.02

0.025

0.03

1/[Oligo-2, ATTTCATTT], µM-1 with inhibitor

without inhibitor

Linear (with inhibitor )

Linear (without inhibitor)

Figure 4: Double-reciprocal plot (1/V vs 1/[S]) of deamination of the DNA substrate (Oligo-2) by A3BCTD-QM-∆L3-AL1swap at different substrate concentrations in the absence and presence of dZcontaining Oligo-9 at 20 µM.

Discussion By means of several complementary binding and activity assays, we have characterized inhibition of selected A3 variants by chemically modified ssDNAs possessing 2'-deoxyzebularine analogs. One finding was that binding of dZ-ssDNA to inactivated proteins in which the active-site glutamic acid is replaced by alanine (Glu72 in A3A, Glu255 in A3BCTD) was significantly reduced in comparison to the substrate. This indicates that the glutamate in the active site is strongly involved in interaction with the transition state of deamination. These data are consistent with a model in which the Glu modifies the TSA by protonation of N3 of the nucleobase causing the addition of a water molecule to the C4 of dZ, as established for CDA54. In addition, our data clearly show an influence of buffer on dissociation constants, with high ionic strength (800 mM) depressing affinity by more than two orders of magnitude relative to medium ionic strength (~100 mM). Our observation that dZMe in the structure of ssDNA did not provide significant inhibition of A3GCTD is consistent with earlier observations that 15 ACS Paragon Plus Environment

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5-Me-cytidine was not deaminated by A3GCTD.51-53 On the other hand, dZ instead of dC in ssDNA produced competitive, micromolar inhibitors of A3GCTD, A3BCTD -QM-∆L3-AL1swap, and A3BCTD DM. The fact that dZ and dZMe used in the same oligo sequence had different inhibitory effects on A3GCTD under identical conditions means that structure of the TSA determines the inhibitory potential of the TSA-containing oligo. Moreover, adjacent nucleotides proximal to the TSA define the selectivity for binding and concomitant inhibition of a particular A3-family member as in case of selective inhibition of A3GCTD by Oligo-7 and not by Oligo-9 (Figure 3A). These sequence-dependent molecular recognition properties provide opportunities for the design of specific inhibitors of A3family members. Through high throughput screening efforts, covalent small molecule A3G inhibitors with low micromolar potencies have been identified33, 55. To date, no small molecule A3A or A3B inhibitors have been reported. Chemically modified ssDNAs have been utilized in previous studies to understand the deamination of cytosine in the absence of structural information of the ssDNA/A3 complex56. Here, we evaluated chemically modified ssDNAs as potential A3 inhibitors and found similar (micromolar) inhibition constants as found for small molecule A3G inhibitors. An approximately 10- to 30-fold decrease of the apparent inhibition constants Ki of dZ-oligos over Km of the corresponding dC-containing substrates was observed in our study. In comparison, zebularine as an individual nucleoside shows 100 times lower Ki in comparison to Km of cytidine for CDA54. This indicates that the preferences for TSA vary between A3 and CDAs. In addition, the strength of binding of the dZ-ssDNA to the enzyme may be mediated by the interactions of surrounding nucleotides with amino acids close to the active site. The latter possibility is supported by the fact that introduction of modified nucleotides in positions -2 to +1 substantially affected the rate of deamination (target dC has number 0, nucleotides in the 5'-direction have a minus sign and nucleotides in the 3'-direction have a plus sign)56. Recent work has revealed that ssDNA adopts a Ushape in order for the target dC to enter the active site of the protein29, 30, 42, such that nucleotides at positions -2, -1 and +1 have strong interactions with the proteins as well. Our previously published NMR-based method of small changes shows additional transient interactions with nucleotides further away from the active site29. This also correlates with our observations that short DNA sequences (5mers) bind much more weakly than longer ssDNAs (>9-mers) to A3A-E72A (Tables 1 and 2) and with the results of other groups.39, 40, 47 The observed inhibition of A3 enzymes by dZ-ssDNAs highlights the importance of Glu72 for A3A (Glu255 for A3BCTD and Glu259 for A3GCTD) in controlling substrate and dZ-ssDNA binding. Therefore, development of A3 inhibitors based on TSAs that specifically react with the active site water requires evaluation on active enzymes in contrast to the common practice of evaluation of binding to inactive active-site mutants.

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Overall, our work shows that transition-state analogs potently inhibit selected A3 variants when incorporated into ssDNA. The inhibition of wild type A3A and full length A3B and A3G is a subject of ongoing investigations. Nevertheless, our results provide a starting point to rationally create new A3 inhibitors, which have a potential to be further developed into adjuvants to be used in anti-viral and anti-cancer treatments since cytidine-containing ssDNA species are not substrates for CDA57, which accepts only individual nucleotides. Thus, our inhibitors to A3 enzymes will not affect primary metabolic functions of CDA. Taking advantage of different preferences of A3 for nucleotides surrounding the reactive 2'-deoxycytidine may also allow development of A3-specific inhibitors, targeting individual family members. Associated Content Supporting Information Experimental details about synthesis of dZ and dZMe modified oligos, protein expression and purification, details of FP, ITC, thermal shift and NMR-based kinetic assays; examples of calculation of inhibition of A3-enzymes by dZ-containing oligos; supplementary tables including thermodynamic parameters obtained from ITC data and rational behind the design of individual oligos; supplementary charts, including ITC data, supplementary figures including data of fluorescence deaminase assays on individual TSAs, representative data of FP assay, sequence alignment of proteins used in this study. Author information Corresponding authors *E-mail: [email protected], [email protected], [email protected] ORCID Geoffrey B. Jameson 0000-0003-4839-0784 Alex M. Ayoub 0000-0003-0341-8747 Hideki Aihara 0000-0001-7508-6230 Reuben S. Harris 0000-0002-9034-9112 Vyacheslav V. Filichev 0000-0002-7383-3025 Daniel A. Harki 0000-0001-5950-931X Elena Harjes 0000-0002-3643-9432 Funding: VVF, EH, GBJ, MVK and SH are grateful for the financial support provided by the Worldwide Cancer Research (grant 16-1197), Massey University Research Fund (MURF 2015, 7003) and Institute of Fundamental Sciences, Massey University. This work was also supported by the National Institutes of Health (R01-GM110129 to DAH & RSH; R01-GM118000 to RSH, HA, and DAH), the University of Minnesota (UMN) Masonic Cancer Center (SPORE-Program Project planning 17 ACS Paragon Plus Environment

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seed grant to DAH, RSH, and HA), the UMN College of Biological Sciences, and the Prospect Creek Foundation (award to DAH & RSH). FB is a recipient of the graduate assistance PhD scholarship awarded by the Institute of Fundamental Sciences, Massey University. The UMN Office of the Vice President for Research is gratefully acknowledged (Equipment Grant-in-Aid to purchase of a BioAutomation MerMade DNA synthesizer). RSH is the Margaret Harvey Schering Land Grant Chair for Cancer Research, a Distinguished University McKnight Professor, and an Investigator of the Howard Hughes Medical Institute. We thank International mobility fund from the Royal Society of New Zealand (IMF-Mau140) for sponsoring the visit of RSH to Massey University to start the collaboration as well as Massey University Research Funding (international visitor, 2016) for sponsoring the visit of DAH to Massey University to design this research.

Conflict of Interest Statement: DAH and RSH are co-founders, shareholders, and consultants of ApoGen Biotechnologies, Inc. HA is a consultant of ApoGen Biotechnologies, Inc. Acknowledgements: We thank M. Carpenter, K. Kurahashi, M. Li, J. McCann, A. Molan, N. Shaban and W. Brown for mentoring and technical training during FB’s visit to the Harris and Aihara laboratories in the University of Minnesota, USA. We would also like to show our gratitude to K. Kurahashi (UMN) for assistance in protein expression and purification. NMR and mass-spectrometry facilities at Massey University and the assistance of Dr. P. J. B. Edwards and D. Lun are gratefully acknowledged.

References: 1) Harris, R. S., and Dudley, J. P. (2015) APOBECs and virus restriction, Virology 479-480, 131-145. 2) Malim, M., and Bieniasz, P. (2012) HIV restriction factors and mechanisms of evasion, Cold Spring Harb Perspectives Med 2, a006940. 3) Izumi, T., Shirakawa, K., and Takaori-Kondo, A. (2008) Cytidine deaminases as a weapon against retroviruses and a new target for antiviral therapy., Mini Rev Med Chem 8, 231-238. 4) Peretti, A., Geoghegan, E. M., Pastrana, D. V., Smola, S., Feld, P., Sauter, M., Lohse, S., Ramesh, M., Lim, E. S., Wang, D., Borgogna, C., FitzGerald, P. C., Bliskovsky, V., Starrett, G. J., Law, E. K., Harris, R. S., Killian, J. K., Zhu, J., Pineda, M., Meltzer, P. S., Boldorini, R., Gariglio, M., and Buck, C. B. (2018) Characterization of BK Polyomaviruses from Kidney Transplant Recipients Suggests a Role for APOBEC3 in Driving In-Host Virus Evolution, Cell Host & Microbe 23, 628635.e627. 5) Vieira, V. C., Leonard, B., White, E. A., Starrett, G. J., Temiz, N. A., Lorenz, L. D., Lee, D., Soares, M. A., Lambert, P. F., Howley, P. M., and Harris, R. S. (2014) Human Papillomavirus E6 Triggers Upregulation of the Antiviral and Cancer Genomic DNA Deaminase APOBEC3B, mBio 5, e02234-02214. 6) Verhalen, B., Starrett, G. J., Harris, R. S., and Jiang, M. (2016) Functional Upregulation of the DNA Cytosine Deaminase APOBEC3B by Polyomaviruses, J Virol 90, 6379-6386. 18 ACS Paragon Plus Environment

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7) Kim, E.-Y., Lorenzo-Redondo, R., Little, S. J., Chung, Y.-S., Phalora, P. K., Maljkovic Berry, I., Archer, J., Penugonda, S., Fischer, W., Richman, D. D., Bhattacharya, T., Malim, M. H., and Wolinsky, S. M. (2014) Human APOBEC3 Induced Mutation of Human Immunodeficiency Virus Type-1 Contributes to Adaptation and Evolution in Natural Infection, PLoS Pathog 10, e1004281. 8) Wood, N., Bhattacharya, T., Keele, B. F., Giorgi, E., Liu, M., Gaschen, B., Daniels, M., Ferrari, G., Haynes, B. F., McMichael, A., Shaw, G. M., Hahn, B. H., Korber, B., and Seoighe, C. (2009) HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC, PLoS Pathog 5, e1000414. 9) Tsibris, A. M., Korber, B., Arnaout, R., Russ, C., Lo, C. C., Leitner, T., Gaschen, B., Theiler, J., Paredes, R., Su, Z., Hughes, M. D., Gulick, R. M., Greaves, W., Coakley, E., Flexner, C., Nusbaum, C., and Kuritzkes, D. R. (2009) Quantitative deep sequencing reveals dynamic HIV1 escape and large population shifts during CCR5 antagonist therapy in vivo, PLoS One 4, e5683. 10) Kohli, R. M., Maul, R. W., Guminski, A. F., McClure, R. L., Gajula, K. S., Saribasak, H., McMahon, M. A., Siliciano, R. F., Gearhart, P. J., and Stivers, J. T. (2010) Local sequence targeting in the AID/APOBEC family differentially impacts retroviral restriction and antibody diversification, J Biol Chem 285, 40956-40964. 11) Rathore, A., Carpenter, M. A., Demir, O., Ikeda, T., Li, M., Shaban, N. M., Law, E. K., Anokhin, D., Brown, W. L., Amaro, R. E., and Harris, R. S. (2013) The local dinucleotide preference of APOBEC3G can be altered from 5'-CC to 5'-TC by a single amino acid substitution, J Mol Biol 425, 4442-4454. 12) Carpenter, M. A., Rajagurubandara, E., Wijesinghe, P., and Bhagwat, A. S. (2010) Determinants of sequence-specificity within human AID and APOBEC3G, DNA Repair 9, 579-587. 13) Stenglein, M., Burns, M., Li, M., Lengyel, J., and Harris, R. (2010) APOBEC3 proteins mediate the clearance of foreign DNA from human cells, Nat Struct Mol Biol 17, 222 - 229. 14) Kohli, R. M., Abrams, S. R., Gajula, K. S., Maul, R. W., Gearhart, P. J., and Stivers, J. T. (2009) A portable hot spot recognition loop transfers sequence preferences from APOBEC family members to activation-induced cytidine deaminase, J Biol Chem 284, 22898-22904. 15) Venkatesan, S., Rosenthal, R., Kanu, N., McGranahan, N., Bartek, J., Quezada, S. A., Hare, J., Harris, R. S., and Swanton, C. (2018) Perspective: APOBEC mutagenesis in drug resistance and immune escape in HIV and cancer evolution, Ann Oncol 29, 563-572. 16) Zou, J., Wang, C., Ma, X., Wang, E., and Peng, G. (2017) APOBEC3B, a molecular driver of mutagenesis in human cancers, Cell & Bioscience 7, 29. 17) Vlachostergios, P. J., and Faltas, B. M. (2018) Treatment resistance in urothelial carcinoma: an evolutionary perspective, Nat Rev Clin Oncol 15, 495-509. 18) Galluzzi, L., and Vitale, I. (2017) Driving to Cancer on a Four-Lane Expressway, Trends in Genetics 33, 491-492. 19) Sieuwerts, A. M., Willis, S., Burns, M. B., Look, M. P., Gelder, M. E. M.-V., Schlicker, A., Heideman, M. R., Jacobs, H., Wessels, L., Leyland-Jones, B., Gray, K. P., Foekens, J. A., Harris, R. S., and Martens, J. W. M. (2014) Elevated APOBEC3B Correlates with Poor Outcomes for EstrogenReceptor-Positive Breast Cancers, Hormones and Cancer 5, 405-413. 20) Law, E. K., Sieuwerts, A. M., LaPara, K., Leonard, B., Starrett, G. J., Molan, A. M., Temiz, N. A., Vogel, R. I., Meijer-van Gelder, M. E., Sweep, F. C., Span, P. N., Foekens, J. A., Martens, J. W., Yee, D., and Harris, R. S. (2016) The DNA cytosine deaminase APOBEC3B promotes tamoxifen resistance in ER-positive breast cancer, Sci Adv 2, e1601737. 21) Olson, M. E., Harris, R. S., and Harki, D. A. (2018) APOBEC Enzymes as Targets for Virus and Cancer Therapy, Cell Chem Biol 25, 36-49. 22) Ko, T. P., Lin, J. J., Hu, C. Y., Hsu, Y. H., Wang, A. H., and Liaw, S. H. (2003) Crystal structure of yeast cytosine deaminase. Insights into enzyme mechanism and evolution, J Biol Chem 278, 19111-19117.

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